Secondary structure inducing potential of beta-amino acids: Torsion angle clustering facilitates comparison and analysis of the conformation during MD trajectories

Guthöhrlein EW, Malesevic M, Majer Z, Sewald N (2007)
BIOPOLYMERS 88(6): 829-839.

Journal Article | Published | English

No fulltext has been uploaded

Author
; ; ;
Abstract
While numerous examples of P-peptides-exclusively composed of (beta-amino acids-have been investigated during the past decade, there are only few reports on the conformational preference of a single (beta-amino acid when incorporated into a cyclopeptide. The conformational bias of (beta-amino acids on the secondary structure of cyclopeptides has been investigated by NMR spectroscopy in combination with distance geometry (DG) and molecular dynamics (MD) calculations using experimental constraints. The atomic coordinate RMSD criterion usually employed for clustering of conformations after DG and MD calculations does not necessarily group similar peptide conformations, as there is an insufficient correlation between atomic coordinates and torsion angles. To improve on this shortcoming and to eliminate any arbitrary decisions during this process, a torsion angle clustering procedure has been implemented. For the cyclic pentapeptides cyclo-(-Val-(beta-Hala-Phe-Leu-Ile-) 1 and cyclo-(-Ser-Pro-Leu-(beta-Hasn-Asp-) 3, the (beta-amino acid is found in the central position of an extended y-turn (pseudo y-turn, psi gamma-turn), while the (beta-Hpro residue in the cyclic hexapeptide cyclo-(-Ser-(beta-HproLeu-Asn-Ile-Asp-) 5 preferentially occupies position i+1 of a pseudo P-turn (T(psi beta-turn). These results furthercorroborate the hypothesis of (beta-amino acids being reliable inducers of secondary structure in cyclic penta- and hexapeptides. They can be employed in the de novo design of biologically active cyclopeptides in pharmaceutical research, since the three-dimensional presentation of pharmacophoric groups in the side chains can be tailored by incorporation of (beta-amino acids in strategic sequential positions. (c) 2007 Wiley Periodicals, Inc.
Publishing Year
ISSN
eISSN
PUB-ID

Cite this

Guthöhrlein EW, Malesevic M, Majer Z, Sewald N. Secondary structure inducing potential of beta-amino acids: Torsion angle clustering facilitates comparison and analysis of the conformation during MD trajectories. BIOPOLYMERS. 2007;88(6):829-839.
Guthöhrlein, E. W., Malesevic, M., Majer, Z., & Sewald, N. (2007). Secondary structure inducing potential of beta-amino acids: Torsion angle clustering facilitates comparison and analysis of the conformation during MD trajectories. BIOPOLYMERS, 88(6), 829-839.
Guthöhrlein, E. W., Malesevic, M., Majer, Z., and Sewald, N. (2007). Secondary structure inducing potential of beta-amino acids: Torsion angle clustering facilitates comparison and analysis of the conformation during MD trajectories. BIOPOLYMERS 88, 829-839.
Guthöhrlein, E.W., et al., 2007. Secondary structure inducing potential of beta-amino acids: Torsion angle clustering facilitates comparison and analysis of the conformation during MD trajectories. BIOPOLYMERS, 88(6), p 829-839.
E.W. Guthöhrlein, et al., “Secondary structure inducing potential of beta-amino acids: Torsion angle clustering facilitates comparison and analysis of the conformation during MD trajectories”, BIOPOLYMERS, vol. 88, 2007, pp. 829-839.
Guthöhrlein, E.W., Malesevic, M., Majer, Z., Sewald, N.: Secondary structure inducing potential of beta-amino acids: Torsion angle clustering facilitates comparison and analysis of the conformation during MD trajectories. BIOPOLYMERS. 88, 829-839 (2007).
Guthöhrlein, E. W., Malesevic, M., Majer, Z., and Sewald, Norbert. “Secondary structure inducing potential of beta-amino acids: Torsion angle clustering facilitates comparison and analysis of the conformation during MD trajectories”. BIOPOLYMERS 88.6 (2007): 829-839.
This data publication is cited in the following publications:
This publication cites the following data publications:

4 Citations in Europe PMC

Data provided by Europe PubMed Central.

Design of cyclic peptides featuring proline predominantly in the cis conformation under physiological conditions.
Malesevic M, Schumann M, Jahreis G, Fischer G, Lucke C., Chembiochem 13(14), 2012
PMID: 22969011
Cyclic RGD peptides interfere with binding of the Helicobacter pylori protein CagL to integrins αVβ3 and α5β1.
Conradi J, Huber S, Gaus K, Mertink F, Royo Gracia S, Strijowski U, Backert S, Sewald N., Amino Acids 43(1), 2012
PMID: 21915696
VCD studies on cyclic peptides assembled from L-α-amino acids and a trans-2-aminocyclopentane- or trans-2-aminocyclohexane carboxylic acid.
Vass E, Strijowski U, Wollschlager K, Mandity IM, Szilvagyi G, Jewginski M, Gaus K, Royo S, Majer Z, Sewald N, Hollosi M., J. Pept. Sci. 16(11), 2010
PMID: 20848613

29 References

Data provided by Europe PubMed Central.

Spectroscopic Detection of Pseudo-Turns in Homodetic Cyclic Penta- and Hexapeptides Comprising β-Homoproline
Malešević, International Journal of Peptide Research and Therapeutics 12(2), 2006
Hybrid Peptides: Expanding the β Turn in Peptide Hairpins by the Insertion of β-, γ-, and δ-Residues
Rai, Chemistry - A European Journal 13(20), 2007
The Constrained Amino Acid β-Acc Confers Potency and Selectivity to Integrin Ligands
Urman, Angewandte Chemie International Edition 46(21), 2007
Conformation of cyclic peptides. Principle concepts and the design of selectivity and superactivity in bioactive sequences by 'spatial screening'
Kessler, Pure and Applied Chemistry 68(6), 1996

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 17922495
PubMed | Europe PMC

Search this title in

Google Scholar